title: Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers.
abstract: A message passing interface (MPI)-based implementation (Autodock4.lga.MPI) of the grid-based docking program Autodock4 has been developed to allow simultaneous and independent docking of multiple compounds on up to thousands of central processing units (CPUs) using the Lamarkian genetic algorithm. The MPI version reads a single binary file containing precalculated grids that represent the protein-ligand interactions, i.e., van der Waals, electrostatic, and desolvation potentials, and needs only two input parameter files for the entire docking run. In comparison, the serial version of Autodock4 reads ASCII grid files and requires one parameter file per compound. The modifications performed result in significantly reduced input/output activity compared with the serial version. Autodock4.lga.MPI scales up to 8192 CPUs with a maximal overhead of 16.3%, of which two thirds is due to input/output operations and one third originates from MPI operations. The optimal docking strategy, which minimizes docking CPU time without lowering the quality of the database enrichments, comprises the docking of ligands preordered from the most to the least flexible and the assignment of the number of energy evaluations as a function of the number of rotatable bounds. In 24 h, on 8192 high-performance computing CPUs, the present MPI version would allow docking to a rigid protein of about 300K small flexible compounds or 11 million rigid compounds.
authors.affiliation: Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Collignon
authors.forename: Roland
authors.initials: R
authors.lastname: Schulz
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
authors.forename: Jerome
authors.initials: J
authors.lastname: Baudry
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003201:Computers; D030562:Databases, Protein; D015195:Drug Design; D057166:High-Throughput Screening Assays / Q000379:methods; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins